Table 1.

Twenty-eight novel loci identified in the genome-wide meta-analysis of kidney stone disease

CHR	Position	Lead SNP	EA/NEA	EAF	OR (95% CI)	P	Gene	Replication
1	150958836	rs267733	A/G	0.845	0.92 (0.89–0.95)	2.07×10−8	ANXA9	5.17×10−3 (rs7551686)
1	186651932	rs113831804	A/T	0.022	1.24 (1.16–1.33)	1.09×10−9	PACERR	9.64×10−4 (rs7516899)*
1	205724302	rs823121	A/G	0.438	1.07 (1.05–1.09)	3.48×10−9	SLC41A1	7.56×10−6 (rs41264867)*
1	220082150	rs884127	A/G	0.404	0.92 (0.9–0.95)	8.93×10−12	SLC30A10	3.00×10−4 (rs77145552)*
3	48861058	rs200495345	A/AT	0.943	1.3 (1.22–1.39)	2.67×10−15	PRKAR2A	2.09×10−1 (rs3895736)
3	51100168	rs191107165	A/G	0.048	0.77 (0.71–0.83)	6.55×10−11	DOCK3	3.23×10−5 (rs72964039)*
3	52124388	rs138789058	T/C	0.065	0.84 (0.79–0.89)	8.01×10−10	POC1A	3.23×10−5 (rs72964039)*
4	3744294	rs440318	A/G	0.547	0.94 (0.92–0.96)	2.68×10−8	ADRA2C	1.22×10−3 (rs35867127)*
4	77505067	rs28454965	A/G	0.504	0.93 (0.91–0.96)	1.37×10−9	SHROOM3	2.97×10−4 (rs7664160)*
4	115498457	rs71606723	A/T	0.717	0.9 (0.88–0.93)	3.45×10−16	UGT8	5.13×10−4 (rs9884467)*
5	51165567	rs55672774	T/C	0.362	1.08 (1.05–1.1)	9.31×10−11	ISL1	6.00×10−5 (rs184643180)*
6	32107851	rs3134962	A/G	0.155	0.9 (0.87–0.93)	1.51×10−11	PRRT1	9.37×10−8 (rs4947328)*
6	43804571	rs729761	T/G	0.296	1.08 (1.06–1.11)	1.79×10−10	VEGFA	1.25×10−4 (rs137924211)*
6	50786008	rs2206271	A/T	0.318	1.08 (1.05–1.11)	9.70×10−11	TFAP2B	1.08×10−5 (rs11961359)*
6	101161812	rs1039031	A/G	0.494	1.07 (1.04–1.09)	5.98×10−9	ASCC3	1.09×10−3 (rs12210312)*
7	142605221	rs4252512	T/C	0.985	0.78 (0.71–0.85)	1.88×10−8	TRPV5	1.05×10−2 (rs11520897)
9	71172306	rs12376362	A/C	0.823	1.09 (1.06–1.12)	8.00×10−9	TMEM252	4.22×10−3 (rs71503670)
9	97585477	rs150891531	T/C	0.086	0.88 (0.84–0.91)	8.73×10−10	AOPEP	7.05×10−7 (rs10993151)*
10	9280394	rs17486892	T/C	0.773	1.08 (1.05–1.11)	1.90×10−8	TCEB1P3	2.08×10−4 (rs1243417)*
10	90142203	rs11202736	A/T	0.680	0.93 (0.91–0.95)	2.47×10−9	RNLS	1.90×10−5 (rs11203100)*
13	96175396	rs57719175	A/G	0.400	0.93 (0.91–0.95)	2.05×10−10	CLDN10	4.58×10−4 (rs61152555)*
15	48500263	rs34819316	A/G	0.005	0.54 (0.43–0.67)	4.59×10−8	SLC12A1	2.52×10−4 (rs117970606)*
15	85719783	rs10852147	T/G	0.319	1.07 (1.04–1.09)	4.35×10−8	PDE8A	4.69×10−3 (rs4887181)
16	88549264	rs55637647	C/G	0.650	0.93 (0.91–0.95)	6.50×10−10	ZFPM1	3.68×10−7 (rs8054971)*
17	44025888	rs242559	A/C	0.808	0.92 (0.89–0.94)	4.22×10−9	MAPT	2.11×10−4 (rs197923)*
19	4335513	rs58169740	T/G	0.683	1.07 (1.05–1.1)	6.74×10−9	STAP2	3.55×10−4 (rs58659609)*
19	46181392	rs1800437	C/G	0.227	0.92 (0.9–0.95)	1.02×10−9	GIPR	5.72×10−5 (rs187967034)*
19	53357172	rs7259073	T/C	0.916	1.13 (1.08–1.18)	3.02×10−8	ZNF468	1.09×10−3 (rs11667654)*

The lead SNP is the variant with the smallest P value within each locus. The gene is the nearby protein-coding gene to the lead SNP.

EA effect allele, NEA non-effect allele, EAF frequency of the effect allele, OR Odds ratio, CI confidence interval.

*suggests the variant with the smallest P value at each novel locus in Japanese population passed the significant threshold (0.05/28).